Cleavage-site motifs in mitochondrial targeting peptides

Although mitochondrial targeting peptides lack a common consensus sequence, a certain bias in the positional distribution of amino acids has recently been found. These patterns seem to be associated with cleavage of the precursor proteins by matrix processing proteases. We have extended the previous studies and found new sequence motifs that are conserved within subgroups of mitochondrial targeting peptides. These motifs have certain common themes, indicating that they are associated with cleavage by one single protease. Two of the conserved patterns have a high predictive value, but even for sequences that do not possess these patterns, a fairly accurate prediction of the cleavage site is shown to be possible. We also suggest that a well-conserved RXY decreases (S/A) pattern may be used to engineer efficiently recognized cleavage sites into uncleaved or artificial mitochondrial targeting peptides.     

Transcending the impenetrable: how proteins come to terms with membranes

In the living cell, proteins are efficiently sorted to a whole range of subcellular compartments. In many cases, sorting specificity is mediated by short 'sorting signals' attached either permanently or transiently to the protein. At long last, a fairly coherent picture of the design and function of many such sorting signals is beginning to emerge.     

How signal sequences maintain cleavage specificity

The specificity of the signal sequence cleavage reaction has been postulated to reside in a signal peptidase active site that can bind only to particular (i, i + 2) pairs of amino acids. In this paper, we present further patterns of non-random amino acid utilization in a region around in vivo cleavage sites, and show that they can be interpreted in terms of selection acting to reduce the number of potential competing sites in the vicinity of the correct one.     

A new method for predicting signal sequence cleavage sites.

A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins.     

Summer Epidemics of Apple Scab: The Relationship between Measurements and their Implications for the Development of Predictive Models and Threshold Levels under Different Disease Control Regimes

A 2‐year study on epidemic progress of apple scab was conducted at Randwijk, the Netherlands, in 1998 and 1999. The summer epidemic caused by conidia was studied instead of the well‐described spring season epidemic originating from ascospores. The aim was to investigate relationships between disease measurements, i.e. disease incidence and severity measures of apple scab, and their implications for the development of predictive models and threshold levels. The study characterized good relationships between the measurements on cultivar Jonagold using regression analyses in three disease control regimes (untreated, organic and integrated). For fruit quality prediction, the relationship between fruit incidence (I_f) and leaf incidence (I_l) in the organic control regime was given by I_f = 1.966 + 0.402 × (I_l) (R² = 0.92). As a result of low level of disease in the integrated control regime, shoot incidence (I_s), with higher values than leaf incidence, was better suited for prediction. The relationship was given by I_f = ?0.162 + 0.028 × (I_s) (R² = 0.91). For the integrated control regime, disease threshold levels were constructed for timing of the final fungicide application. If an apple grower wants to keep fruit infection under 1% incidence (harvest scab threshold), the timing of the final fungicide application (action threshold) should correspond to 4% shoot scab incidence at the beginning of August. The results are compared with similar studies and their biological interpretation is discussed.     

Translation and messenger RNA secondary structure

The possibility of translation being influenced by the messenger RNA secondary structure is investigated with the aid of a stochastic model. Simulations indicate that, at least for certain mRNA's, the mean ribosomal passage time decreases as the mean number of ribosomes on the messenger is increased. Furthermore, large variations in the passage times are found, in accordance with recent experimental results.     

Models for mRNA translation: theory versus experiment.

Three models for mRNA translation are discussed in the light of available experimental data. It is concluded that the elongation rates vary along a messenger, possibly as a result of a coupling between ribosome movement and mRNA secondary structure. Some promising areas of further experimentation are indicated.